Training Material List
Handles creating, reading and updating training materials.
GET /api/trainingmaterial/?format=api&offset=40&ordering=-description
{ "count": 144, "next": "https://catalogue.france-bioinformatique.fr/api/trainingmaterial/?format=api&limit=20&offset=60&ordering=-description", "previous": "https://catalogue.france-bioinformatique.fr/api/trainingmaterial/?format=api&limit=20&offset=20&ordering=-description", "results": [ { "id": 117, "name": "Chip-seq: Peak calling tutorial", "description": "The aim is to :\nUnderstand how to process reads to obtain peaks (peak-calling).\nBecome familiar with differential analysis of peaks\nIn practice :\nObtain dataset from GEO\nAnalyze mapped reads\nObtain set(s) of peaks, handle replicates\nDifferential analysis of peak\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://dputhier.github.io/EBA_2015_ChIP-Seq/tutorial/01_peak_calling/peak_calling_tutorial.html", "fileName": "missing.txt", "topics": [], "keywords": [ "Chip-Seq", "Peak calling", "NGS" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/698/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/644/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/721/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/512/?format=api" ] }, { "id": 100, "name": "REPET: TEdannot Tutorial", "description": "TEannot is able to annote a genome using DNA sequences library. This library can be a predicted TE library built by TEdenovo\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://urgi.versailles.inra.fr/Tools/REPET/TEannot-tuto", "fileName": "missing.txt", "topics": [], "keywords": [ "genomics", "Annotation" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": "CeCILL", "maintainers": [] }, { "id": 4, "name": "Support tools for rapid adoption of compact identifiers in the publishing process", "description": "\n \n\nSupport tools for rapid adoption of compact identifiers in the publishing process\n \n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ressources.france-bioinformatique.fr/sites/default/files/videos/scorms/support-tools_78a0/scormcontent/index.html", "fileName": "missing.txt", "topics": [], "keywords": [ "biohackaton 2018" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2019-03-21", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/668/?format=api" ] }, { "id": 81, "name": "Assessing microbial biogeography by using a metagenomic approach", "description": "Soils are highly complex ecosystems and are considered as one of the Earth’s main reservoirs of biological diversity. Bacteria account for a major part of this biodiversity, and it is now clear that such microorganisms have a key role in soil functioning processes. However, environmental factors regulating the diversity of below-ground bacteria still need to be investigated, which limits our understanding of the distribution of such bacteria at various spatial scales. The overall objectives of this study were: (i) to determine the spatial patterning of bacterial community diversity in soils at a broad scale, and (ii) to rank the environmental filters most influencing this distribution.\nThis study was performed at the scale of the France by using the French Soil Quality Monitoring Network. This network includes more than 2,200 soil samples along a systematic grid sampling. For each soil, bacterial diversity was characterized using a pyrosequencing approach targeting the 16S rRNA genes directly amplified from soil DNA, obtaining more than 18 million of high-quality sequences.\nThis study provides the first estimates of microbial diversity at the scale of France, with for example, bacterial richness ranging from 555 to 2,007 OTUs (on average: 1,289 OTUs). It also provides the first extensive map of bacterial diversity, as well as of major bacterial taxa, revealing a bacterial heterogeneous and spatially structured distribution at the scale of France. The main factors driving bacterial community distribution are the soil physico-chemical properties (pH, texture...) and land use (forest, grassland, crop system...), evidencing that bacterial spatial distribution at a broad scale depends on local filters such as soil characteristics and land use when regarding the community (quality, composition) as a whole. Moreover, this study also offers a better evaluation of the impact of land uses on soil microbial diversity and taxa, with consequences in terms of sustainability for agricultural systems.\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://www.france-bioinformatique.fr/sites/default/files/videos/scorms/metagenomics16/session_4/Assessing_microbial_biogeography_by_using_a_metagenomic_approach/scormcontent/index.html", "fileName": "missing.txt", "topics": [], "keywords": [ "Metagenomics" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2016-12-16", "dateUpdate": null, "licence": "CC BY-NC-ND", "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/709/?format=api" ] }, { "id": 51, "name": "Eukaryotic small RNA", "description": "\n \n\nSmall RNAseq data analysis for miRNA identification\n \n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ressources.france-bioinformatique.fr/sites/default/files/sRNA-Seq.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "RNA-seq" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2016-11-23", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/642/?format=api" ] }, { "id": 1, "name": "SG-ONT-slides", "description": "Slides used for the training \"\t\r\nIntroduction to Oxford Nanopore Technology data analyses\"", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://southgreenplatform.github.io/trainings//files/ont_2021.pdf", "fileName": "ont_2021.pdf", "topics": [], "keywords": [], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2022-01-24", "dateUpdate": "2022-01-24", "licence": "Creative Commons Attribution 4.0 International License", "maintainers": [] }, { "id": 137, "name": "Linux slides", "description": "Slides for linux session (genotoul bioinfo facility)", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://bioinfo.genotoul.fr/wp-content/uploads/Formation_LINUX_GenoToul_2024.pdf", "fileName": "Formation_LINUX_GenoToul_2024.pdf", "topics": [], "keywords": [ "Operating systems" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "Novice", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": "CC BY-NC-SA", "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/300/?format=api" ] }, { "id": 139, "name": "Cluster Slides", "description": "Slides for Cluster training (bioinfo genotoul facility)", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://bioinfo.genotoul.fr/wp-content/uploads/Formation_cluster_SLURM_2024.pdf", "fileName": "Formation_cluster_SLURM_2024.pdf", "topics": [], "keywords": [ "Cluster" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "Novice", "providedBy": [ { "id": 22, "name": "Genotoul-bioinfo", "url": "https://catalogue.france-bioinformatique.fr/api/team/Genotoul-bioinfo/?format=api" } ], "dateCreation": null, "dateUpdate": null, "licence": "CC BY-NC-SA", "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/300/?format=api" ] }, { "id": 76, "name": " Reconstructing genomes from metagenomes: The holy grail of microbiology", "description": "Shotgun metagenomics provides insights into a larger context of naturally occurring microbial genomes when short reads are assembled into contiguous DNA segments (contigs). Contigs are often orders of magnitude longer than individual sequences, offering improved annotations, and key information about the organization of genes in cognate genomes. Several factors affect the assembly performance, and the feasibility of the assembly-based approaches varies across environments. However, increasing read lengths, novel experimental approaches, advances in computational tools and resources, and improvements in assembly algorithms and pipelines render the assembly-based metagenomic workflow more and more accessible. The utility of metagenomic assembly remarkably increases when contigs are organized into metagenome-assembled genomes (MAGs). Often-novel MAGs frequently provide deeper insights into bacterial lifestyles that would otherwise remain unknown as evidenced by recent discoveries. The increasing rate of the recovery of MAGs presents new opportunities to link environmental distribution patterns of microbial populations and their functional potential, and transforms the field of microbiology by providing a more complete understanding of the microbial life, ecology, and evolution.\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://www.france-bioinformatique.fr/sites/default/files/videos/scorms/metagenomics16/session_5/Reconstructing_genomes_from_metagenomes_the_holy_grail_of_microbiology/scormcontent/index.html", "fileName": "missing.txt", "topics": [], "keywords": [ "Metagenomics" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2016-12-16", "dateUpdate": null, "licence": "CC BY-NC-ND", "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/665/?format=api" ] }, { "id": 61, "name": "Differential gene expression analysis : Practical part", "description": "RNA-seq: Differential gene expression analysis practical session\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://www.france-bioinformatique.fr/sites/default/files/R01b_EBA2016_TP_RNA-seq.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "genomics", "RNA-seq" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2016-11-22", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/371/?format=api" ] }, { "id": 111, "name": "Chip-seq: Discovering motifs in peaks with RSAT", "description": "Read mapping: from raw reads to aligned reads.\nPeak calling: from aligned reads to regions/peaks of high read density.\nChIP-seq annotation\nIdentification of genes related to the peaks.\nProfiles of ChIP-seq reads around reference points (TSS, histone marks,).\nFunctional enrichment of the genes related to the peaks.\n\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ecole-bioinfo-aviesan.sb-roscoff.fr/sites/ecole-bioinfo-aviesan.sb-roscoff.fr/files/files/ChIP-seq_motifs_EBA2015_JvH.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "Motif analysis", "Chip Seq", "NGS" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/624/?format=api" ] }, { "id": 98, "name": "A Quick and focused overview of R data types and ggplot2 syntax", "description": "R and RStudio overview.\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://genoweb.toulouse.inra.fr/~formation/15_FROGS/April2016/R_phyloseq/ModuleIntroInitR.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "R", "Statistics", "Graphical analysis" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2016-04-01", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/415/?format=api" ] }, { "id": 94, "name": "Searching for sequence: Tutorial", "description": "Quick Search is dedicated to a quick search for sequences or sequence families in the databases available on the PBIL server. It is an alternative to WWW Query which allows more complex queries. Quick Search allows you to retrieve sequences or sequence families associated to a single word without specifying what is this word. You can enter indifferently a keyword, a sequence name or accession number, or a taxa name.\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://www.prabi.fr/spip.php?article17", "fileName": "missing.txt", "topics": [], "keywords": [ "genomics", "Pattern recognition" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": null, "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/715/?format=api" ] }, { "id": 32, "name": "Docker and Galaxy", "description": "Questions\nWhy Docker? What is it?\nHow to use Docker?\nHow to integrate Galaxy in Docker to facilitate its deployment?\nObjectives\nDocker basics\nGalaxy Docker image (usage)\nGalaxy Docker (internals)\nGalaxy flavours\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://galaxyproject.github.io/training-material//Admin-Corner/slides/galaxy_docker", "fileName": "missing.txt", "topics": [], "keywords": [ "Docker", "Galaxy" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2017-01-19", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/663/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/187/?format=api" ] }, { "id": 47, "name": "ToolShed upload and tool-iuc PR", "description": "Questions\nWhat is a Tool Shed?\nHow to install tools and workflows from a Tool Shed into a Galaxy instance?\nWhat are the Tool Shed repository types?\nHow to publish with Planemo?\nObjectives\nDiscover what is a Tool Shed\nBe able to install tools and workflows from a Tool Shed into a Galaxy instance\nBe able to publish tools with Planemo\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "https://igbmc.github.io/egdw2017/day2/toolshed/index.html", "fileName": "missing.txt", "topics": [], "keywords": [ "Galaxy" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2017-01-17", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/677/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/689/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/362/?format=api" ] }, { "id": 48, "name": "Tool development and integration into Galaxy", "description": "Questions:\nWhat is a tool for Galaxy?\nHow to build a tool/wrapper with the good practices?\nHow to deal with the tool environment?\n \nObjectives:\nDiscover what is a wrapper and its structure\nUse the Planemo utilities to develop a good wrapper\nDeal with the dependencies\nWrite functional tests\nMake a tool ready for publishing in a ToolShed\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://galaxyproject.github.io/training-material/Dev-Corner/slides/tool_integration.html", "fileName": "missing.txt", "topics": [], "keywords": [ "Galaxy" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2017-01-16", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/663/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/677/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/689/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/362/?format=api" ] }, { "id": 43, "name": "Galaxy Interactive Tour", "description": "Questions\nWhat is a Galaxy Interactive Tour?\nHow to create a Galaxy Interactive Tour?\nObjectives\nDiscover what is a Galaxy Interactive Tour\nBe able to create a Galaxy Interactive Tour\nBe able to add a Galaxy Interactive Tour in a Galaxy instance\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://galaxyproject.github.io/training-material/Dev-Corner/slides/interactive_tour.html", "fileName": "missing.txt", "topics": [], "keywords": [ "Galaxy" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2017-01-18", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/677/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/689/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/662/?format=api" ] }, { "id": 45, "name": "Galaxy Visualisation - Slides", "description": "Questions\n\n\n\tHow can visualization plugins benefit science?\n\n\n\nObjectives\n\n\n\tImplement a first Galaxy visualization\n\tUnderstand the client side vs. server side principle\n\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://galaxyproject.github.io/training-material/Dev-Corner/slides/visualizations.html", "fileName": "missing.txt", "topics": [], "keywords": [ "Galaxy" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2017-01-18", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/690/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/691/?format=api" ] }, { "id": 65, "name": "Chip-seq Analysis", "description": "Quality, normalisation and peak calling\n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://www.france-bioinformatique.fr/sites/default/files/C01_ChIP_SEQ_EBA_2016-11-22.pdf", "fileName": "missing.txt", "topics": [], "keywords": [ "genomics", "Chip-Seq" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2016-11-22", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/695/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/696/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/697/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/698/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/512/?format=api" ] }, { "id": 5, "name": "Putting structured data into individual entry pages in biological database", "description": "\n \n\nPutting structured data into individual entry pages in biological database\n \n", "communities": [], "elixirPlatforms": [], "doi": null, "fileLocation": "http://ressources.france-bioinformatique.fr/sites/default/files/videos/scorms/putting-structured_bf31/scormcontent/index.html", "fileName": "missing.txt", "topics": [], "keywords": [ "biohackaton 2018" ], "audienceTypes": [], "audienceRoles": [], "difficultyLevel": "", "providedBy": [], "dateCreation": "2019-03-21", "dateUpdate": null, "licence": null, "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/669/?format=api" ] } ] }